BioLab

BioLab is a stochastic model-checker for BioNetGen models. You provide, as input to BioLab, a BioNetGen model, a property expressed in linear temporal logic, and a probability. BioLab tells you whether the property is satisfied with probability less than the given probability or greater than the given probability.

You can download BioLab for Mac OS X here. After downloading it, just unzip it. BioLab is pre-installed; you can run it immediately, using the following instructions.

Defining Linear Temporal Logic Properties for BioLab

Linear Temporal Logic (LTL) formulas must be in negation normalized form to be interpreted correctly by BioLab (i.e., negations are pushed inside as far as possible).

The syntax for the LTL formulae:

"{" <variable> <relop> <constant> "}" - a relational expression:

<variable> is a variable name, either the name "time" or the name of an observable in the BioNetGen model;

<relop> is a relational operator (<, <=, =, >, >=);

<constant> is any constant expression legal in the C programming language.

The entire expression must be contained in the curly braces.

f AND g - both f and g are true: f and g are any negation normal LTL formulas

f OR g - either f or g is true: f and g are any negation normal LTL formulas